A Review on the Techniques for Characterizing and Predicting Human Genomic DNA Methylation

Hao      Zheng; Shi-Wen      Jiang; Hongwei      Wu

Abstract

Epigenetic modification refers to heritable changes in genotypes or phenotypes through biochemical modifications without altering the underlying DNA sequence. In humans, DNA methylation is a major epigenetic modification that adds a methyl group mainly to the carbon-5 position of the cytosine pyrimidine ring in the cytosine guanine dinucleotide. This epigenetic modification is crucial to normal development and cellular differentiation as well as a number of key processes including genomic imprinting, X-chromosome inactivation, suppression of repetitive elements, and tumorigenesis. Recently, a lot of resources and efforts have been devoted to the DNA methylation profiling of human genome based on biochemical experiments or computational prediction. Here, we provide a review on these experimental and computational techniques, and large-scaled DNA methylation data sets and databases. While the description of the biochemical techniques is mainly to provide an overview of the biological background, we focus more on the computational techniques, particularly on the data resources, methodologies and problems that have been studied. Our goal is to provide a guidance for future bioinformatics research on DNA methylation.

Keywords: DNA methylation, computational epigenetics, prediction, Bisulfite Conversion, Enzyme, lymphoblastoid cell, skeletal muscle, fetal liver, pancreas,